14 15 Word count, abstract: 233 16 Word count, manuscript: 2157 17 Highlights 18 • A metagenomics protocol employing virus capture probes was validated and retrospectively 19 applied to 41 hematological adult and pediatric patients presenting with encephalitis of 20 unknown aetiology 21 • Viral enrichment by capture probes increased sensitivity of viral metagenomics on 22 cerebrospinal fluid samples 100 -10.000 fold, compared to unenriched metagenomic 23 sequencing 24 • In 12% of hematological patients with encephalitis of unknown origin, a virus was detected 25 by viral metagenomics, which was not found by routine diagnostics 26 • Viral metagenomics represents a valuable addition to the diagnostics repertoire for 27 hematological patients with suspected CNS infection 28 3 29 Abstract 30Metagenomic sequencing is a powerful technique that enables detection of the full spectrum of 31 pathogens present in any specimen in a single test. Hence, metagenomics is increasingly being 32 applied for detection of viruses in clinical cases with suspected infections of unknown etiology and a 33 large number of relevant potential causes. This is typically the case in patients presenting with 34 encephalitis, in particular when immunity is impaired by underlying disorders. 35In this study, viral metagenomics has been applied to a cohort of hematological patients with 36 encephalitis of unknown origin. 37Since viral loads in cerebrospinal fluid of patients with encephalitis are generally low, the technical 38 performance of a metagenomic sequencing protocol enriched by capture probes targeting all known 39 vertebrate viral sequences was studied. Subsequently, the optimized viral metagenomics protocol 40 was applied to a cohort of hematological patients with encephalitis of unknown origin. 41 Viral enrichment by capture probes increased the viral sequence read count of metagenomics on 42 cerebrospinal fluid samples 100 -10.000 fold, compared to unenriched metagenomic sequencing. 43In five out of 41 (12%) hematological patients with encephalitis, a virus was detected by viral 44 metagenomics which had not been detected by current routine diagnostics. BK polyomavirus, 45 hepatitis E virus, human herpes virus-6 and Epstein Barr virus were identified by this unbiased 46 metagenomic approach. 47This study demonstrated that hematological patients with encephalitis of unknown origin may 48 benefit from early viral metagenomics testing as a single step approach. 49 50
Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log10 at disbalanced positions in samples with high viral loads (Ct values ≤ 23). Phylogenetic analyses of consensus sequences showed clustering independent of the workflow used. The proportion of SARS-CoV-2 reads in relation to background sequences, as a (cost-)efficiency metric, was the highest for the EasySeq protocol. The hands-on time was the lowest when using EasySeq and ONT protocols, with the latter additionally having the shortest sequence runtime. In conclusion, the studied protocols differed on a variety of the studied metrics. This study provides data that assist laboratories when selecting protocols for their specific setting.
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